If you understand how to manipulate a magnetic field properly, you can get it to work. You would need to design it so the pole pieces (don't use ND's as the poles) don't pull as much, or use smaller magnets than a ceramic or AlNiCo would use.

I wanted to use the Nd magnets as the poles and place the pickup inside the bass body so the magnets could be farer from the strings and don't pull so much. I'm also interested how such a pickup would sound.I want to use to thin magnet bars to built a 6 string bass humbucker with colis splited for 3 strings.

The issue is going to be the pickups aperature, (how large the magnetic field is at the strings) Using very strong magnets further away is going to have a relatively huge aperature which will tend to make the sound very "complex" as a minimum and likely "distorted/fuzzy". The other possible result would be a very "flat" sounding pickup if it's a dual coil HB design and the field picks up too many cancelling harmonics...